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Fusion Protein:C16orf72-ABAT

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: C16orf72-ABAT
	FusionPDB ID: 11027
	FusionGDB2.0 ID: 11027
		Hgene	Tgene
	Gene symbol	C16orf72	ABAT
	Gene ID	29035	18
	Gene name	chromosome 16 open reading frame 72	4-aminobutyrate aminotransferase
	Synonyms	PRO0149	GABA-AT\|GABAT\|NPD009
	Cytomap	16p13.2	16p13.2
	Type of gene	protein-coding	protein-coding
	Description	UPF0472 protein C16orf72	4-aminobutyrate aminotransferase, mitochondrial(S)-3-amino-2-methylpropionate transaminase4-aminobutyrate transaminaseGABA aminotransferaseGABA transaminaseGABA transferasegamma-amino-N-butyrate transaminasegamma-aminobutyrate aminotransferase
	Modification date	20200313	20200313
	UniProtAcc	Q14CZ0 Main function of 5'-partner protein:	P80404 Main function of 5'-partner protein: FUNCTION: Catalyzes the conversion of gamma-aminobutyrate and L-beta-aminoisobutyrate to succinate semialdehyde and methylmalonate semialdehyde, respectively. Can also convert delta-aminovalerate and beta-alanine.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000327827,	ENST00000425191, ENST00000563215, ENST00000567812, ENST00000569156, ENST00000268251, ENST00000396600,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 6 X 4=144	7 X 9 X 4=252
	# samples	8	9
	** MAII score	log2(8/144*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/252*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: C16orf72 [Title/Abstract] AND ABAT [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: C16orf72 [Title/Abstract] AND ABAT [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	C16orf72(9197116)-ABAT(8851614), # samples:3
Anticipated loss of major functional domain due to fusion event.	C16orf72-ABAT seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. C16orf72-ABAT seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	ABAT	GO:0009448	gamma-aminobutyric acid metabolic process	15528998

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:9197116/chr16:8851614)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.

Retention analysis results of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features, are available here.

Fusion gene breakpoints across C16orf72 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across ABAT (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000327827

C16orf72

chr16

9197116

ENST00000268251

ABAT

chr16

8851614

5312

980

2166

720

ENST00000327827

C16orf72

chr16

9197116

ENST00000396600

ABAT

chr16

8851614

5312

980

2166

720

ENST00000327827

C16orf72

chr16

9197116

ENST00000268251

ABAT

chr16

8851613

5312

980

2166

720

ENST00000327827

C16orf72

chr16

9197116

ENST00000396600

ABAT

chr16

8851613

5312

980

2166

720

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000327827	ENST00000268251	C16orf72	chr16	9197116	+	ABAT	chr16	8851614	+	0.003795204	0.9962048
ENST00000327827	ENST00000396600	C16orf72	chr16	9197116	+	ABAT	chr16	8851614	+	0.003795204	0.9962048
ENST00000327827	ENST00000268251	C16orf72	chr16	9197116	+	ABAT	chr16	8851613	+	0.003795204	0.9962048
ENST00000327827	ENST00000396600	C16orf72	chr16	9197116	+	ABAT	chr16	8851613	+	0.003795204	0.9962048

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for C16orf72-ABAT

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
C16orf72	chr16	9197116	ABAT	chr16	8851613	980	325	TDLQPFREAIALHGYSHPALLKLIQQ
C16orf72	chr16	9197116	ABAT	chr16	8851614	980	325	TDLQPFREAIALHGYSHPALLKLIQQ

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Potential FusionNeoAntigen Information of C16orf72-ABAT in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

C16orf72-ABAT_9197116_8851613.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:01	HGYSHPAL	0.998	0.8887	12	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:02	HGYSHPAL	0.998	0.8887	12	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B08:01	HGYSHPAL	0.9969	0.5753	12	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B44:03	REAIALHGY	0.9991	0.9495	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:01	LHGYSHPAL	0.9987	0.8842	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B38:02	LHGYSHPAL	0.9954	0.9613	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B38:01	LHGYSHPAL	0.9938	0.9582	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:24	LHGYSHPAL	0.9902	0.6143	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-A02:13	ALHGYSHPA	0.9891	0.6107	10	19
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:01	HGYSHPALL	0.9862	0.8634	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:02	HGYSHPALL	0.9862	0.8634	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-A02:27	ALHGYSHPA	0.9844	0.5023	10	19
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-A02:38	ALHGYSHPA	0.9843	0.7208	10	19
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:06	LHGYSHPAL	0.9748	0.8176	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:02	LHGYSHPAL	0.9699	0.8655	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:01	LHGYSHPAL	0.9699	0.8655	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:01	REAIALHGY	0.9154	0.8161	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B52:01	HGYSHPALL	0.9028	0.9095	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B48:01	HGYSHPALL	0.7004	0.6219	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B15:18	LHGYSHPAL	0.6343	0.5524	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B15:03	REAIALHGY	0.1351	0.5008	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-A30:08	HGYSHPALLK	0.9942	0.6637	12	22
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B38:02	LHGYSHPALL	0.986	0.9569	11	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B38:01	LHGYSHPALL	0.9843	0.9552	11	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:03	HGYSHPAL	0.9651	0.8725	12	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:07	HGYSHPALL	0.9995	0.9725	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C15:04	HGYSHPALL	0.9995	0.8681	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:19	HGYSHPALL	0.9994	0.9785	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C15:06	HGYSHPALL	0.9993	0.8813	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:08	HGYSHPALL	0.9987	0.8619	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:09	LHGYSHPAL	0.9986	0.7484	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:12	LHGYSHPAL	0.9984	0.8952	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C04:06	HGYSHPALL	0.9967	0.9623	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:05	LHGYSHPAL	0.996	0.8624	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C12:12	HGYSHPALL	0.9888	0.9351	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C08:04	HGYSHPALL	0.9875	0.9714	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C08:13	HGYSHPALL	0.9875	0.9714	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:05	HGYSHPALL	0.9752	0.9406	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:14	HGYSHPALL	0.9748	0.9745	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C06:03	HGYSHPALL	0.9746	0.9906	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C12:04	HGYSHPALL	0.9722	0.9888	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C12:16	HGYSHPALL	0.9615	0.9621	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C08:03	HGYSHPALL	0.9453	0.9817	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:13	HGYSHPALL	0.9392	0.9088	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:29	HGYSHPALL	0.9214	0.9152	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:27	HGYSHPALL	0.9172	0.9356	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:95	HGYSHPALL	0.9083	0.6325	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:19	HGYSHPALL	0.8884	0.791	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C02:06	HGYSHPALL	0.8272	0.933	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:03	HGYSHPALL	0.7943	0.8537	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B51:07	HGYSHPALL	0.7681	0.7813	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C01:17	HGYSHPALL	0.7585	0.9651	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C01:30	HGYSHPALL	0.5731	0.9612	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B14:03	LHGYSHPAL	0.3868	0.8239	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:05	HGYSHPAL	0.9998	0.9091	12	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B08:18	HGYSHPAL	0.9969	0.5753	12	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B35:24	EAIALHGY	0.9847	0.7935	7	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B35:43	EAIALHGY	0.9681	0.7775	7	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:04	EAIALHGY	0.9615	0.6203	7	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:07	EAIALHGY	0.9381	0.5272	7	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C15:09	HGYSHPALL	0.9995	0.8681	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:05	HGYSHPALL	0.9994	0.9054	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:17	HGYSHPALL	0.9993	0.9504	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B44:26	REAIALHGY	0.9991	0.9495	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C15:05	HGYSHPALL	0.9991	0.9373	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B44:13	REAIALHGY	0.9991	0.9495	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B44:07	REAIALHGY	0.9991	0.9495	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:67	HGYSHPALL	0.9988	0.9639	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C15:02	HGYSHPALL	0.9987	0.8943	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:31	LHGYSHPAL	0.9983	0.8875	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:04	HGYSHPALL	0.9983	0.9767	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:03	HGYSHPALL	0.9983	0.9767	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-A02:03	ALHGYSHPA	0.997	0.5122	10	19
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C04:04	HGYSHPALL	0.9964	0.9648	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:04	HGYSHPALL	0.9942	0.9266	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B38:05	LHGYSHPAL	0.9938	0.9582	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C16:01	HGYSHPALL	0.9894	0.9741	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C03:06	HGYSHPALL	0.9875	0.9763	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C06:17	HGYSHPALL	0.9858	0.9885	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C06:02	HGYSHPALL	0.9858	0.9885	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C12:03	HGYSHPALL	0.9839	0.9734	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C16:04	HGYSHPALL	0.9786	0.9788	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B15:09	LHGYSHPAL	0.9767	0.663	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:11	REAIALHGY	0.9683	0.7948	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C06:06	HGYSHPALL	0.9503	0.9856	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C08:01	HGYSHPALL	0.9453	0.9817	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C16:02	HGYSHPALL	0.9433	0.9901	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:22	HGYSHPALL	0.9402	0.6539	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:04	REAIALHGY	0.9256	0.8358	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:08	REAIALHGY	0.9247	0.6029	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C12:02	HGYSHPALL	0.9241	0.9638	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:05	REAIALHGY	0.9154	0.8161	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:06	REAIALHGY	0.9133	0.8136	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:03	REAIALHGY	0.9128	0.8049	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C07:01	HGYSHPALL	0.8869	0.6213	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C06:08	HGYSHPALL	0.8744	0.983	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C01:02	HGYSHPALL	0.7493	0.9649	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C01:03	HGYSHPALL	0.7058	0.9578	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-C17:01	HGYSHPALL	0.7045	0.9684	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B39:11	LHGYSHPAL	0.674	0.7627	11	20
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B35:28	REAIALHGY	0.6303	0.8125	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B07:13	HGYSHPALL	0.4633	0.8424	12	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B15:53	REAIALHGY	0.3973	0.6313	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B48:02	REAIALHGY	0.1583	0.7876	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B15:54	REAIALHGY	0.0697	0.5833	6	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-A30:01	HGYSHPALLK	0.9933	0.851	12	22
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B38:05	LHGYSHPALL	0.9843	0.9552	11	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B15:09	LHGYSHPALL	0.9681	0.6903	11	21
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	HLA-B18:11	FREAIALHGY	0.8991	0.8246	5	15

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Potential FusionNeoAntigen Information of C16orf72-ABAT in HLA II

C16orf72-ABAT_9197116_8851613.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0103	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0109	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0113	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0115	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0117	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0121	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0129	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0447	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0447	DLQPFREAIALHGYS	1	16
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0454	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0454	DLQPFREAIALHGYS	1	16
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0474	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0902	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0902	DLQPFREAIALHGYS	1	16
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0902	QPFREAIALHGYSHP	3	18
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0902	TDLQPFREAIALHGY	0	15
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-0903	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-1001	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-1003	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-1130	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-1130	DLQPFREAIALHGYS	1	16
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB1-1130	QPFREAIALHGYSHP	3	18
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB5-0102	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB5-0103	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB5-0108N	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB5-0112	LQPFREAIALHGYSH	2	17
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB5-0112	DLQPFREAIALHGYS	1	16
C16orf72-ABAT	chr16	9197116	chr16	8851613	980	DRB5-0112	QPFREAIALHGYSHP	3	18

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Fusion breakpoint peptide structures of C16orf72-ABAT

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
7758	REAIALHGYSHPAL	C16orf72	ABAT	chr16	9197116	chr16	8851613	980

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of C16orf72-ABAT

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	7758	REAIALHGYSHPAL	-7.9962	-8.1096
HLA-B14:02	3BVN	7758	REAIALHGYSHPAL	-5.70842	-6.74372
HLA-B52:01	3W39	7758	REAIALHGYSHPAL	-6.83737	-6.95077
HLA-B52:01	3W39	7758	REAIALHGYSHPAL	-4.4836	-5.5189
HLA-A11:01	4UQ2	7758	REAIALHGYSHPAL	-10.0067	-10.1201
HLA-A11:01	4UQ2	7758	REAIALHGYSHPAL	-9.03915	-10.0745
HLA-A24:02	5HGA	7758	REAIALHGYSHPAL	-6.56204	-6.67544
HLA-A24:02	5HGA	7758	REAIALHGYSHPAL	-5.42271	-6.45801
HLA-B44:05	3DX8	7758	REAIALHGYSHPAL	-7.85648	-8.89178
HLA-B44:05	3DX8	7758	REAIALHGYSHPAL	-5.3978	-5.5112
HLA-A02:01	6TDR	7758	REAIALHGYSHPAL	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of C16orf72-ABAT

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
C16orf72-ABAT	chr16	9197116	chr16	8851613	10	19	ALHGYSHPA	CTCTGCATGGTTACAGCCACCCCGCCC
C16orf72-ABAT	chr16	9197116	chr16	8851613	11	20	LHGYSHPAL	TGCATGGTTACAGCCACCCCGCCCTGC
C16orf72-ABAT	chr16	9197116	chr16	8851613	11	21	LHGYSHPALL	TGCATGGTTACAGCCACCCCGCCCTGCTGA
C16orf72-ABAT	chr16	9197116	chr16	8851613	12	20	HGYSHPAL	ATGGTTACAGCCACCCCGCCCTGC
C16orf72-ABAT	chr16	9197116	chr16	8851613	12	21	HGYSHPALL	ATGGTTACAGCCACCCCGCCCTGCTGA
C16orf72-ABAT	chr16	9197116	chr16	8851613	12	22	HGYSHPALLK	ATGGTTACAGCCACCCCGCCCTGCTGAAAC
C16orf72-ABAT	chr16	9197116	chr16	8851613	5	15	FREAIALHGY	TCCGGGAAGCCATAGCTCTGCATGGTTACA
C16orf72-ABAT	chr16	9197116	chr16	8851613	6	15	REAIALHGY	GGGAAGCCATAGCTCTGCATGGTTACA
C16orf72-ABAT	chr16	9197116	chr16	8851613	7	15	EAIALHGY	AAGCCATAGCTCTGCATGGTTACA

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
C16orf72-ABAT	chr16	9197116	chr16	8851613	0	15	TDLQPFREAIALHGY	CTGATTTGCAACCCTTCCGGGAAGCCATAGCTCTGCATGGTTACA
C16orf72-ABAT	chr16	9197116	chr16	8851613	1	16	DLQPFREAIALHGYS	ATTTGCAACCCTTCCGGGAAGCCATAGCTCTGCATGGTTACAGCC
C16orf72-ABAT	chr16	9197116	chr16	8851613	2	17	LQPFREAIALHGYSH	TGCAACCCTTCCGGGAAGCCATAGCTCTGCATGGTTACAGCCACC
C16orf72-ABAT	chr16	9197116	chr16	8851613	3	18	QPFREAIALHGYSHP	AACCCTTCCGGGAAGCCATAGCTCTGCATGGTTACAGCCACCCCG

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Information of the samples that have these potential fusion neoantigens of C16orf72-ABAT

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
STAD	C16orf72-ABAT	chr16	9197116	ENST00000327827	chr16	8851613	ENST00000268251	TCGA-VQ-A922

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Potential target of CAR-T therapy development for C16orf72-ABAT

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to C16orf72-ABAT

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to C16orf72-ABAT

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)